Convergent evolution of complex traits in distantly related lineages is commonly attributed to diverse molecular pathways. Here, we provide evidence for a shared genetic mechanism underlying the repeated evolution of compound leaves across angiosperms over ~160 million years. Through macroevolutionary analysis of leaf forms in 44 914 angiosperm species, we identified at least 54 independent origins of compound leaves in 63 families. Comparative genomic analysis of 414 high-quality genomes shows that among all gene families analyzed, only KNOTTED1-like HOMEOBOX (KNOX) exhibits consistent expansion in compound-leaved lineages. This expansion is predominantly driven by whole-genome duplications (WGDs), with KNOXI and KNOXM loci preferentially retained across lineages. Functional assays further reveal opposing roles for KNOX subclasses: KNOXI/KNOXM promote, whereas KNOXII suppresses, compound leaf development. Notably, apparent counterexamples-simple-leaved species with unexpectedly high KNOX counts-are attributable to expansion of the inhibitory KNOXII subclass, thus reinforcing rather than contradicting the model. However, a rare exception occurs within a small clade of Fabaceae, where compound leaf development depends on LEAFY instead of KNOXI genes. Overall, our findings demonstrate that preferential retention of KNOXI/M subfamilies after WGD is a recurrent, quantifiable route linking ancient genome duplications to repeated morphological innovation across flowering plants.
Guo et al. (Wed,) studied this question.